The Molecular Phenotyping core provides instrumentation, training, and services for in vitro cell phenotyping. Specifically, we provide facilities and training for automated nucleic acids purification, microarray analysis, quantitative PCR, and automated immunofluorescence cell marker analysis and screening. In addition to maintaining facilities essential for the many NIH-funded investigators working at MMCRI, planned developments such as resources for analysis of next generation sequencing data and laboratory automation for high density microplate formats will ensure that the core keeps in step with investigators' needs. An efficient workflow for the analysis of gene expression from RNA preparation through transcriptome analysis, and validation of candidate genes has been established. The core facility provides equipment, training, and supplies for all steps in the process with the exception of microarray processing, which is provided by Vermont Genetics Network in a regional collaborative agreement. Both manual and automated epifluorescence microscopy is also provided by the facility. Currently we provide live cell time-lapse microscopy, and microscopy based screening in 6- to 96-well formats, and additional applications such as cell cycle analysis are in development. The core provides image analysis workstations running Metamorph and Image J, and training in specific applications of these software packages. Quantitative image analysis of tissue immunostaining is being provided in collaboration with the Histopathology Core (Lindner). Future developments of our transcriptome analysis capabilities will be in the following areas: i) Transition from 96- to 384-well format. Essential equipment including 384 well real-time PCR instrument and liquid handling station is available in the facility, and users are currently piloting the new platform, ii) Providing an analysis platform for Next Generation Sequencing data. In the cellular analysis area we will be focusing on increasing the number of analyses we can provide users of our automated microscopy platform. Furthermore, we will be transitioning to a 384 well format for microscopy-based screening applications. Longer term core development will be based on feedback from the user base, and input from the internal and external advisory committees of the COBRE.